This fix+comments was originally made by Alexey Kopytov

LP bug #1035225 / MySQL bug #66301: INSERT ... ON DUPLICATE KEY UPDATE +
innodb_autoinc_lock_mode=1 is broken

The problem was that when certain INSERT ... ON DUPLICATE KEY UPDATE
were executed concurrently on a table containing an AUTO_INCREMENT
column as a primary key, InnoDB would correctly reserve non-overlapping
AUTO_INCREMENT intervals for each statement, but when the server
encountered the first duplicate key error on the secondary key in one of
the statements and performed an UPDATE, it also updated the internal
AUTO_INCREMENT value to the one from the existing row that caused a
duplicate key error, even though the AUTO_INCREMENT value was not
specified explicitly in the UPDATE clause. It would then proceed with
using AUTO_INCREMENT values the range reserved previously by another
statement, causing duplicate key errors on the AUTO_INCREMENT column.

Fixed by changing write_record() to ensure that in case of a duplicate
key error the internal AUTO_INCREMENT counter is only updated when the
AUTO_INCREMENT value was explicitly updated by the UPDATE
clause. Otherwise it is restored to what it was before the duplicate key
error, as that value is unused and can be reused for subsequent
successfully inserted rows.

sql/sql_insert.cc:
  Don't update next_insert_id to the value of a row found during ON DUPLICATE KEY UPDATE.
sql/sql_parse.cc:
  Added DBUG_SYNC
sql/table.h:
  Added next_number_field_updated flag to detect changing of auto increment fields.
  Moved fields a bit to get bool fields after each other (better alignment)

sql/sql_insert.cc

@@ -329,7 +329,7 @@ static int check_insert_fields(THD *thd, TABLE_LIST *table_list,
 
 
 /*
-  Check update fields for the timestamp field.
+  Check update fields for the timestamp and auto_increment fields.
 
   SYNOPSIS
     check_update_fields()
@@ -342,6 +342,9 @@ static int check_insert_fields(THD *thd, TABLE_LIST *table_list,
     If the update fields include the timestamp field,
     remove TIMESTAMP_AUTO_SET_ON_UPDATE from table->timestamp_field_type.
 
+   If the update fields include an autoinc field, set the
+   table->next_number_field_updated flag.
+
   RETURN
     0           OK
     -1          Error
@@ -353,7 +356,9 @@ static int check_update_fields(THD *thd, TABLE_LIST *insert_table_list,
 {
   TABLE *table= insert_table_list->table;
   my_bool timestamp_mark;
+  my_bool autoinc_mark;
   LINT_INIT(timestamp_mark);
+  LINT_INIT(autoinc_mark);
 
   if (table->timestamp_field)
   {
@@ -365,6 +370,19 @@ static int check_update_fields(THD *thd, TABLE_LIST *insert_table_list,
                                           table->timestamp_field->field_index);
   }
 
+  table->next_number_field_updated= FALSE;
+
+  if (table->found_next_number_field)
+  {
+    /*
+      Unmark the auto_increment field so that we can check if this is modified
+      by update_fields
+    */
+    autoinc_mark= bitmap_test_and_clear(table->write_set,
+                                        table->found_next_number_field->
+                                        field_index);
+  }
+
   /* Check the fields we are going to modify */
   if (setup_fields(thd, 0, update_fields, MARK_COLUMNS_WRITE, 0, 0))
     return -1;
@@ -386,6 +404,18 @@ static int check_update_fields(THD *thd, TABLE_LIST *insert_table_list,
       bitmap_set_bit(table->write_set,
                      table->timestamp_field->field_index);
   }
+
+  if (table->found_next_number_field)
+  {
+    if (bitmap_is_set(table->write_set,
+                      table->found_next_number_field->field_index))
+      table->next_number_field_updated= TRUE;
+
+    if (autoinc_mark)
+      bitmap_set_bit(table->write_set,
+                     table->found_next_number_field->field_index);
+  }
+
   return 0;
 }
 
@@ -1563,6 +1593,7 @@ int write_record(THD *thd, TABLE *table,COPY_INFO *info)
   MY_BITMAP *save_read_set, *save_write_set;
   ulonglong prev_insert_id= table->file->next_insert_id;
   ulonglong insert_id_for_cur_row= 0;
+  ulonglong prev_insert_id_for_cur_row= 0;
   DBUG_ENTER("write_record");
 
   info->records++;
@@ -1709,6 +1740,7 @@ int write_record(THD *thd, TABLE *table,COPY_INFO *info)
             INSERT query, which is handled separately by
             THD::arg_of_last_insert_id_function.
           */
+          prev_insert_id_for_cur_row= table->file->insert_id_for_cur_row;
           insert_id_for_cur_row= table->file->insert_id_for_cur_row= 0;
           trg_error= (table->triggers &&
                       table->triggers->process_triggers(thd, TRG_EVENT_UPDATE,
@@ -1716,9 +1748,22 @@ int write_record(THD *thd, TABLE *table,COPY_INFO *info)
           info->copied++;
         }
 
-        if (table->next_number_field)
-          table->file->adjust_next_insert_id_after_explicit_value(
-            table->next_number_field->val_int());
+        /*
+          Only update next_insert_id if the AUTO_INCREMENT value was explicitly
+          updated, so we don't update next_insert_id with the value from the
+          row being updated. Otherwise reset next_insert_id to what it was
+          before the duplicate key error, since that value is unused.
+        */
+        if (table->next_number_field_updated)
+        {
+          DBUG_ASSERT(table->next_number_field != NULL);
+
+          table->file->adjust_next_insert_id_after_explicit_value(table->next_number_field->val_int());
+        }
+        else
+        {
+          table->file->restore_auto_increment(prev_insert_id_for_cur_row);
+        }
         goto ok_or_after_trg_err;
       }
       else /* DUP_REPLACE */